This is the 3rd thread I have made since starting my first pirate game. This one is real weird.

I had 100% control over 2 planets (not enough money to build anything though). I then discover an abandon colony ship. I send it off to colonize a world. Here's where it gets weird. It colonizes, and its not under my control. But the two planets that I have 100% control over now are available in my colonies screen, as if I own them (but I cannot order them to do anything). So my colony ship settle a world as an independent? And what's the two colonies in my colonies screen, if not mine?

I know settling a colony ship won't make the planet yours.. its still full of someone else's colonists and they don't want to be part of your pirate empire (although they seem to be willing to join any old terrestrial empire). I have no idea about the two colonies under your control though.

This sounds like a bug. If you have a save game I recommend submitting it in the tech support forum.

I reloaded a save from after I acquired the colony ship, but before it settled - and it is making me a lair. It will not reproduce the strangness again. The colony ship now settles an independent world, and does nothing to my colonies screen.